Structure of PDB 6ccv Chain C Binding Site BS02

Receptor Information
>6ccv Chain C (length=1099) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLVGSDRWRQAAIDRGE
ENPVGGLEEVLAELSPIEDFSGSMSLSFSDPRFDEVKASVDECKDKDMTY
AAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQL
VRSPGVYFDETIDKSTEKTLHSVKVIPGRGAWLEFVRIDRKRRQPVTVLL
KALGWTNEQIVERFGFSEIMMGTLEKDTTSGTDEALLDIYRKLRPGEPPT
KESAQTLLENLFFKEKRYDLARVGRYKVNKKLTLTEEDVVATIEYLVRLH
EGQTSMTVPGGVEVPVEVDDIDHFGNRRLRTVGELIQNQIRVGLSRMERV
VRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGL
THKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGS
LSVYARVNPFGFIETPYRKVENGVVTDQIDYLTADEEDRHVVAQANSPTD
ENGRFTEDRVMVRKKGGEVEFVSADQVDYMDVSPRQMVSVATAMIPFLEH
DDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVADKTGV
IEEVSADYITVMADDGTRQSYRLRKFARSNHGTCANQRPIVDAGQRVEAG
QVIADGPCTQNGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTS
IHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDG
DILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIG
IRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKIL
PVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKAGWNIDVA
AGVPDWASKLPEELYSAPADSTVATPVFDGAQEGELAGLLGSTLPNRDGE
VMVDADGKSTLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPY
SMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGR
VKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIEMR
Ligand information
Ligand IDRFP
InChIInChI=1S/C43H58N4O12/c1-21-12-11-13-22(2)42(55)45-33-28(20-44-47-17-15-46(9)16-18-47)37(52)30-31(38(33)53)36(51)26(6)40-32(30)41(54)43(8,59-40)57-19-14-29(56-10)23(3)39(58-27(7)48)25(5)35(50)24(4)34(21)49/h11-14,19-21,23-25,29,34-35,39,49-53H,15-18H2,1-10H3,(H,45,55)/b12-11+,19-14+,22-13-,44-20+/t21-,23+,24+,25+,29-,34-,35+,39+,43-/m0/s1
InChIKeyJQXXHWHPUNPDRT-WLSIYKJHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](C=C\C=C(/C(=O)Nc(c2O)c(c3O)\C=N\N5CCN(CC5)C)\C)C)O)C)O)C)OC(=O)C)C)OC)C)O
ACDLabs 10.04O=C4c5c2c(O)c(\C=N\N1CCN(C)CC1)c3c(O)c2c(O)c(c5OC4(OC=CC(OC)C(C(OC(=O)C)C(C)C(O)C(C)C(O)C(C=CC=C(C(=O)N3)C)C)C)C)C
CACTVS 3.341CO[CH]1C=CO[C]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)C(=CC=C[CH](C)[CH](O)[CH](C)[CH](O)[CH](C)[CH](OC(C)=O)[CH]1C)C)c(C=NN5CCN(C)CC5)c(O)c4c3C2=O
CACTVS 3.341CO[C@H]1\C=C\O[C@@]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)\C(=C/C=C/[C@H](C)[C@H](O)[C@@H](C)[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]1C)C)c(\C=N\N5CCN(C)CC5)c(O)c4c3C2=O
OpenEye OEToolkits 1.5.0Cc1c(c2c3c4c1OC(C4=O)(OC=CC(C(C(C(C(C(C(C(C=CC=C(C(=O)Nc(c2O)c(c3O)C=NN5CCN(CC5)C)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
FormulaC43 H58 N4 O12
NameRIFAMPICIN
ChEMBLCHEMBL374478
DrugBankDB01045
ZINCZINC000169621223
PDB chain6ccv Chain C Residue 1205 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6ccv Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.
Resolution3.05 Å
Binding residue
(original residue number in PDB)		Q426 Q429 F430 D432 H442 R445 S447 L449 R456 I488 R604 H671
Binding residue
(residue number reindexed from 1)		Q386 Q389 F390 D392 H402 R405 S407 L409 R416 I448 R564 H631
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
Biological Process
GO:0006351 DNA-templated transcription
GO:0046677 response to antibiotic
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ccv, PDBe:6ccv, PDBj:6ccv
PDBsum6ccv
PubMed30297823
UniProtP60281|RPOB_MYCS2 DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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